Epigenetics in Action: Methylation profiling in medicine

One of the ultimate goals of genetic research is the eventual application of medicine and medical techniques resulting from advances in the basic sciences. One such aspect of this application involves the use of PCR methylation assays as a diagnostic for genetic disease. The study performed by Peñaherrera et al. at the University of British Colombia looks into the feasibility of using a quantitative analysis of methylation levels on chromosome 7 as a means of diagnosing patients with the rare genetic disorder, Russell Silver Syndrome. Wikipedia defines Russell Silver Syndrome (RSS) as a type of dwarfism, effecting between 1 in 100,000 to 1 in 3,000 births. Its cause is unclear, but is believed to be a genetic defect, possibly due to an unnecessary X inactivation.

This case is a good example of the potential for epigenetics in medicine. While the genetic code is pretty much set in stone after cellular differentiation, epigenetic factors however, could be altered. Although this study only looks as methylation as a new medical diagnostic tool to screen for RSS, and admittedly there are still issues regarding consistency, it is exciting to see more practical applications for our understanding genetics.

As a personal note; while I am excited about the potential for epigenetics I feel that we are still a long way away from reaching what I feel is the holy grail of applied genetics, or in this case epigenetics, and that is the use of epigenetic techniques such as methylation, acetylation, etc. to cure diseases such as RSS. If we could somehow control epigenetic expression, we would have far more power over many inherent chronic diseases. As someone afflicted with tourette's Syndrome the field of epigenetic medicine is certainly appealing. Tourette's is believed to be an inherited disorder so there is little in the way of hope to cure it as the genetic level without epigenetic tools.

Citation: Penaherrera MS, Weindler S, Van Allen MI, Yong S-L, Metzger DL, McGillivray B, Boerkoel C, Langlois S, Robinson WP. 2010. Methylation profiling in individuals with Russell–Silver syndrome. Am J Med Genet Part A 152A:347–355.

UC Davis researchers develop new test for fragile X syndrome

Fragile X syndrome is the number one cause of inherited mental retardation in humans. People with Fragile X syndrome experience deficits in learning, behavior, motor skills, sensory systems, and speech. The extent to which each individual will be affected depends largely on how extensive the mutation is on their X chromosome and the affected person’s gender. Additionally, most individuals with the syndrome are screened for whether or not they also have autism as the two disorders are commonly found to be comorbid.

Fragile X syndrome is caused by the slipped mispairing of three nucleotides CGG in the FMR1 gene. This mutation leads to a deficit in the FMR1 Protein as the expanded mutation silences the gene. Lacking this protein, normal communication between nerve cells cannot occur and people with the syndrome often have substantial cognitive delays as a result. Because the FMR1 gene is on the X chromosome, boys are more likely to be affected than girls as a result of inheriting a mother’s affected X chromosome. Likewise, because these mothers pass on the affected X chromosome to their sons, the mothers themselves are often mildly affected with increased anxiety and slight behavioral abnormalities. Girls who inherit one affected X chromosome from either parent will often have mild effects as the other X chromosome can make up for some of the deficit.

At UC Davis, both the MIND Institute and the Center for the Mind and Brain do research on the behavioral and molecular abnormalities associated with the syndrome. A new genetic test, developed by Paul Hagerman at the MIND Institute, is called ELISA and was created to measure the level of FMR1 protein expressed in individuals who carry the gene mutation. This test will better allow individuals to be diagnosed with the syndrome so they may therefore receive earlier treatment for the disorder. Decreased FMRP levels have already been associated with other disorders in development, behavior, anxiety, Fragile-X associated tremor/ataxia syndrome, ovarian deficiencies, and ADHD. It is being discussed whether testing for Fragile X syndrome would be beneficial to add to the standard neonatal tests which are already administered at birth.

The fact that UC Davis is associated with the MIND institute is invaluable to students who are interested in genetic disorders. People come from all over the world to visit Drs. Paul and Randi Hagerman as they are experts in the study of Fragile X syndrome and are directors of the Fragile X Syndrome Treatment and Research Center. I have personally been involved in research on fragile X syndrome as a research assistant at the Center for the Mind and Brain and have been able to apply a lot of what I have learned in genetics and psychology to the internship.

References:

Brown, Phyllis. UC Davis researchers develop new test for fragile X syndrome. Insciences Organisation. 2009 [8 June 2010]. <http://insciences.org/article.php?article_id=5897>

Iwahashi, C., Tassone, F., Hagerman, R.J., Yasui, D., Parrott, G., Nguyen, D., Mayeur, G., Hagerman, P.J. A Quantitative ELISA Assay for the Fragile X Mental Retardation 1 Protein. The Journal of Molecular Diagnostics. 2009 [8 June 2010] Vol. 11(4). <http://jmd.amjpathol.org/cgi/content/short/11/4/281>

THE IMPACT OUR GENES HAVE IN LOSING WEIGHT

Are people overweight because they lack the will-power to go through an effective workout at the gym? Do some people have a much harder struggle while trying to lose wieght because of the information encoded in their genes? To answer these questions we explore, "The Truth about Genetics and Weight Loss," by Caroline J. Cederquist.
For starters, it is important to take into account the myriad of other features such as height and eye-color that is already controlled by genes. Moreover, according to Cederquist, "researchers have identified specific combinations of genes that appear to correlate very strongly with fat retention even in spite of, exercise."
In a study, a group involving post-menopausal females were divided into a control and excercise-intervention group. In this particular group, the women were asked to workout for five days a week for forty-five minutes, and eat whatever they usually ate. At the conclusion of the study, the researchers found that the fat-loss of severalindividuals were not backed up by the amount of time that they spent in the gym compared to other individuals.
After examining the genetic data of the individuals, researchers found two genes, CYP19 and COMT that stood-out.The researchers found that even one CYP19 gene along with its variants did not associate with abdominal fat, but having two did correlate to a higher decrease in the BMI (Body Mass Index) of the individual.Also, atleast one of these CYP19 genes along with a certain strain of COMT correlated to an even larger decrease in BMI.
However, the researchers also found out that while those with this particular CYP19 combination lost more fat in shorter time periods, they also gained more fat in shorter amounts of time. The detailed mechanisms of theseprocesses are not fully understood for there to be made any other conclusions.
So whats the bottom line? Calorie input= Calorie output, you are what you eat... are explanations that do not take into accountthe detailed aspects of human genetics. People simply need to be able to learn about how they react to certain foodsand excercise, and adapt their behaviors to that knowledge. In the end, it is harder for some people to lose weight,but that does not mean that they can't make it atleast just a little easier on themselves.

News Article Website:
http://newsblaze.com/story/20051207150658nnnn.nb/topstory.html

Research Article: http://biblioteca.sp.san.gva.es/biblioteca/publicaciones/MATERIAL/METABUSQUEDAS/MUJER/15229337.PDF

to test or not to test? ...that is the question

A great deal of research is being done on the decision making process as to whether or not mothers should undergo prenatal testing. The answer seemed quite obvious to me, why wouldn’t you want to make sure your child was healthy…right?

First it’s important to distinguish that there are two types of prenatal testing: invasive and non-invasive. A non-invasive prenatal test, for example, is an ultrasound. An ultrasound is a procedure that uses high-frequency sound waves to examine a woman's abdomen and pelvic cavity, creating a picture (known as a sonogram) of the baby and placenta. Invasive procedures, which include amniocentesis or chorionic villus sampling (CVS), tend to be diagnostic tests to determine if specific genetic disorders may be present in the baby. An amniocentesis, for instance, is a procedure where a sample of amniotic fluid is collected through a needle from the amniotic sac. The amniotic fluid contains cells shed by the fetus, and is sent to the laboratory for analysis. Prenatal testing, depending on the particular test, occurs throughout the three trimesters of pregnancy. The American Pregnancy Association website provides detailed profiles on the major prenatal tests, divided into trimester-specific tests. For more information you can visit: http://www.americanpregnancy.org/prenataltesting/.

So, why did I choose this topic? Well, my future aspirations are to become a genetic counselor. A genetic counselor is a healthcare professional that provides information and support to families who have members with birth defects/genetic disorders or to families who may be at risk for a variety of inherited conditions. They identify at risk families, investigate the problem, interpret information about the disorder, analyze inheritance patterns and risks of recurrence, and finally, they assess available options with the family. They also serve as educators and a resource for other healthcare professionals and for the general public[1]. This, of course, all applies to helping pregnant women make informed decisions based on test results, and hopefully reduce any decisional conflict they might have.

However, it is important to consider all of the medical, ethical and social concerns that come with prenatal screening/diagnostic testing. All aspects have to be taken into account because this is an extremely touchy subject. Examples include:

-It is important to be sensitive to their beliefs as well as respect their wishes, remaining unbiased in the process.

-It is imperative the mother has a chance to voice her opinion, but if both parents do not see eye to eye it can complicate the situation.

-Certain ethical decisions may have to be made concerning the life of the baby and/or the life of the mother.

Researchers at the University of California San Francisco conducted a study exploring the decision making process involved with invasive prenatal testing after infertility[2]. Researchers found that a history of infertility affects the decision making process about whether or not to undergo invasive prenatal testing. The results of the study would reveal valuable information for heath care providers and genetic counselors and could help in how they should approach apprehensive patients conflicted with the decision, minimizing conflict and thereby enhance informed choices. After questioning 180 pregnant women (who had a history of infertility) results revealed: 69% of the women declined testing; 42% of the women declined prenatal testing on the grounds that infertility had made them unwilling to take the risk of potentially having a miscarriage as a result of the test; 26% reported that testing was unnecessary because they would accept any baby regardless; only approximately 6% of the women felt medically informed enough to weigh their options clearly and opted for the testing. Several variables, both social and ethical, went into their decision making process.

Given that this study focused solely on women with fertility issues we can hardly conclude that these results reflect the decisions of the majority of women in the US, nor do they reflect the general opinion on prenatal testing. Still the process of prenatal screening/diagnostic testing is controversial and raises many ethical issues. This is a very touchy subject, especially when considering the ethical and social aspects. I think that in the scientific and medical community there is a constant battle between science and faith/belief/emotion, etc…. How do you set your own beliefs aside and acknowledge or go along with those of others? As a future genetic counselor I look forward to exploring this dichotomy and helping families through such a process. Personally I’m an advocate of prenatal testing. I’d prefer to know that my child is healthy and safe rather than have to face potentially losing it early in life or having it grow up and live with difficulties the rest of their life. One thing is for certain, it is important that we educate the public and keep families aware so that they may make informed decisions.

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[1] http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genecounseling.shtml

[2] Caleshu, Colleen; Shiloh, Shoshana; Price, Cristofer; Sapp, Julie; Biesecker, Barbara. “Invasive prenatal testing decisions in pregnancy after infertility”. Prenatal Diagnosis. Volume 30, Issue 6. June 2010, Pages: 575-581

Is Addiction wired to our Genes?

Is Addiction wired into our Genes?

According to the Genetics of Addiction, provided by Addiction and Recovery.org, “addiction is due 50 percent to genetic predisposition and 50 percent to poor coping skills.” In one study comparing the likelihood of becoming addicted between identical and non-identical twins, the study shows if one identical twin was addicted to alcohol, the other has a higher chance of becoming addicted as well; however, one non-identical twin was addicted to alcohol, the other twin does not show increased probability of addiction. Three similar papers based on studies of more than 140,000 people have been published online in the journal Nature Genetics. "These variances in the sequence that we have discovered do not have impact on whether you begin to smoke or not," Lead author Kari Stefansson said.


In human population, only 1% of the genes are different from person to person. Researchers identified 11 chromosomes as the probable locations of genes prone to drug abuse and alcohol addiction. Dr. George Uhl and colleagues at NIDA's Intramural Research Program (IRP) in Baltimore, Maryland identified 89 genes to drug abuse and dependence. We have gene variations between drug addicts and non-addicts; however, their research is inconclusive, and there is no clear indication of a certain gene causing a person to become addictive.We all has the genetic predisposition for addiction because there is an evolutionary advantage to that. Some people have certain genes which are more prone to alcohol abuse, cigarette or drugs, but those people are not necessarily addicts. People who have good coping skills and self-control understand the damages of addictions and can stay away from harmful substances. On the other hand, even though some people start with a low genetic predisposition for addiction, repeated moderate use of substances can permanently rewire their brain and make them prone to addiction. Study shows children of alcoholic parents are eight times more likely to become addicted alcohol themselves, but it’s not clear whether it’s due to genetic predisposition or simply environmental effects.


All three articles conclude genes do not necessarily result in addiction. The two on smoking suggest certain genes might increase the change of becoming addicted; the article about drug abuse suggest there are unknown varations between drug-addicts and non-addicts, but the effects are unknown. So it goes back to the beginning, genetic factors only contribute partially to addiction, there are many other factors, such as environmental, family history, life style, and copping skills, etc. I would say we do not have to get ourselves tested for those addiction genes, if we don’t want to become an addict, stay away from alcohol, drugs, and cigarettes in the first place.


links:


The Genetics of Addiction
http://www.addictionsandrecovery.org/is-addiction-a-disease.htm


Can't quit smoking? Blame your genes
By Ashley Hall
http://www.abc.net.au/news/stories/2010/04/26/2882621.htm

Addiction – Blame It on Genes
http://www.ygoy.com/index.php/addiction-blame-it-on-genes/

Proof that the UK > US

Cancer Research UK, the leading cancer charity in the United Kingdom, has begun a project to analyze tumors of cancer patients to cover a wide array of genetic defects. In doing so, they hope to provide individualized therapy for the patients, especially when it comes to medication. By implementing breakthrough discoveries in the field of pharmacogenetics, the centers around the country hope to catalog and classify the tumor according to specific genetic mutations that it carries. Then, using new-age cancer drugs that target specific genetic mutations in cancerous cells, the doctors can avoid expensive treatments that will provide little benefit. The major difference between cancer knowledge ten years ago and cancer knowledge now is that enough genetic markers and drugs have been discovered so that being tested is much more likely to give useful information. The main goal of this new initiative seems to be to cut cost from the British National Health Service, allow for more effective treatments in patients, and build a database of different types of cancer and how effective certain treatments are against each type.

Honestly, I feel the article is being a little optimistic. While certain drugs like Herceptin are mentioned in the article and are certainly effective, most of them are antibodies and cancers can develop a resistance to them like any other drug. Furthermore, such treatments are expensive and may have trouble dealing with the early stages of breast cancer. Finally, the NHS which is overseeing the program is a government run, publically funded healthcare system, meaning that it is an extension of government bureaucracy and that late stage cancers (which these specially developed drugs are most effective against) may claim the patient’s life while waiting for treatment. Another problem that may arise is that a program like this needs time to show its effectiveness as the staff running the centers may not have a large amount of experience in dealing with the work involved in testing all of these patients; as a pilot scheme, it may only last one or two years until the Department of Health decides that it is not showing enough results and shut it down.

Even still, the benefits of the program are substantial if it is successfully implemented. Pharmacogenetics has been a booming field ever since the human genome was unlocked. Successful application and testing of drugs developed through this principle serves to further enrich the field and may lead to the ultimate goal of cheap, personalized drugs for the average citizen. If such a program were implemented in the United States, it might bring even more benefits as the overall cancer rate in the US is much higher than that in the UK. If future advances in pharmacogenetics and stratified medicines continue at their current pace, it might be plausible to eventually have a cure for most common types of cancers.

Sources Used:

http://news.bbc.co.uk/2/hi/health/10224252.stm

http://en.wikipedia.org/wiki/Trastuzumab

http://en.wikipedia.org/wiki/National_Health_Service_(England)

http://www.nhs.uk/Pages/HomePage.aspx

http://www.cancer.org/docroot/STT/content/STT_1x_Cancer_Facts_Figures_2010.asp

http://info.cancerresearchuk.org/cancerstats/incidence/commoncancers/index.htm

Sea Urchins - A Possible Model Organism?

Related to the model organisms we discuss in class, new evidence has come out within the past couple of years indicating that sea urchins may be used in genetic studies to help understand various human diseases. Indirectly, this article poses the idea that sea urchins could possibly serve as a new model organism. Despite being invertebrates and lacking various organisms such as a nose, eyes, and ears, the sea urchin shares more than 7000 genes with humans. Scientists are hoping that this degree of similarity between humans and sea urchins may help to uncover possible ways to fight—and hopefully someday, prevent—various life-threatening diseases. Due to its simplicity, the sea urchin is proving that it can be an asset to future genetic studies. Its short generation time and capability to produce up to 20 million progeny in its lifetime are some characteristics that indicate just how much potential this small-sized organism can have in the field of genetics.

One of the most interesting characteristics of the sea urchin is its long life span. A single sea urchin can live up to 100 years! This lifespan is far greater than any other model organism currently being studied. What is interesting about the sea urchin is that it has been determined they can live for such a long time because of their strong immune systems. Because of its relatively long lifespan, scientists are hoping that they can study the immune system and possibly uncover various ways in which diseases can be fought. In fact, according to the article, sea urchins have innate immunity, similar to humans. Innate immunity describes the inborn ability of an organism to resist contracting a particular disease (Webster’s Dictionary). The difference between the immune system of humans and the immune system of sea urchins is that humans acquire additional immunities over the course of their lives by being exposed to different pathogens, viruses and other disease-causing agents while sea urchins do not. What is fascinating about the similarity between the innate immunities of both sea urchins and humans is the evolution of both of their immune systems over time. The question boggling the minds of researchers today is how exactly sea urchins are able to live for so long without acquiring any additional immunities over their lifetime. Finding the answer to this question could prove to be a positive step in the right direction towards fighting human diseases.

From this article, there seems to be great potential in the research of the sea urchin genome. From studying the 7000 genes that sea urchins and humans have in common, human medicine could see a potential huge breakthrough in the way medicine is used to fight and prevent many life-threatening human diseases.

Link to article: http://www.sciencedaily.com/videos/2007/0304-sea_urchins_reveal_medical_mysteries.htm

Haploid Plants

One of the main hurdles in genetic analysis of plants is the necessity of inbreeding for several generations to create stable lines for a given mutation. This necessity stems from the plant’s ploidy level, which ranges from diploid, which we are very familiar with, to more complex polyploid individuals. One way to make this process more streamlined would be to produce haploid plants which can then be converted to diploid. We would then have a homozygous individual, bypassing many generations of breeding. Achieving this may seem unfamiliar in plants, but the underlying mechanisms are explained clearly in the article.

There are a few ways to produce haploid plants (Arabidopsis thalania, in this case), but the one discussed in this article is via elimination of one parental genome after fertilization. This can happen when one of the parent's centromeric regions on chromosomes doesn’t attach well to the mitotic spindle, making those chromosomes more likely to be lost, leaving only a single set left for the plant. Researchers took advantage of this observation by making a null version a gene coding for a centromeric histone protein, CENH3. This protein is an ortholog to the human CENPA, which we discussed in class. When a male or female CENH3 null mutant is crossed with a normal plant, the mutant’s genome is eliminated, and a haploid individual can be produced.

The next step for the haploid plant is conversion to diploid, which would give the desired homozygous product. For this to occur, a chance event of non-reductive meiosis is required. At the end of meiosis I, chromosomes segregate equally to either side of the cell during anaphase. In this case, our haploid individual has 5 chromosomes, which segregate randomly in a few possible patterns; 2 -3 or 4-1, for example. Tetrads formed by these segregations are often aneuploid, and thus inviable. If 5-0 segregation is observed, however, the cell is a usual product of meiosis I, and after meiosis II, viable gametes are produced. If the plant is self fertilized using these gametes, we now have an individual homozygous for the exact same set of genes!

This discovery has great potential for applications in more efficient research in plant sciences, but there are social and economic implications as well. It provides an interesting option for seed companies like Monsanto (which has a headquarters in Davis). The CENH3 gene is conserved in all eukaryotes, meaning this procedure could be applied to popular crop plants like maize or soybean. This could make it much easier for companies to produce sterile lines of hybrid seed, which must be re-purchased by farmers each time a new crop is planted. This ability of companies like Monsanto ensures their maximum control of industrial level farming, which is becoming a more and more controversial issue in our time.

This topic sparked my interest when I overheard a conversation at my internship about producing haploid Arabidopsis plants. For the blog, I decided to investigate this concept and, to my surprise, discovered an article in Nature written by a UC Davis professor, Simon Chan, and a postdoc in his lab, Maruthachalam Ravi. It's quite exciting to know that the research responsible for this discovery happened right here on campus.

link to article: http://www.nature.com/nature/journal/v464/n7288/full/nature08842.html#B2

(I think you may have to log in through the library website's VPN, then search for this issue of Nature, which is Vol 464, 25 March 2010)

New Genetic Loci Associated with Type 2 Diabetes Risk

Diabetes mellitus is a chronic condition characterized by high levels of sugar in the blood which affects 2.8% of the world population. Type 2 Diabetes results from insulin resistance which may be combined with reduced insulin secretion (impaired beta cell function) and accounts for 90-95% of the U.S. diabetes population. Insulin is a hormone that causes cells in the liver, muscle, and fat tissue to take up glucose from the blood, so reduced insulin secretion or insulin resistance will result in higher blood glucose levels.

The researchers in this report conducted association studies concentrating on the identification of genetic variants that affect fasting glucose levels in adult non-diabetics of European descent. They ended up identifying nine new SNPs associated with fasting glucose levels and one SNP associated with insulin resistance, as well as confirmed a number of previously-found associations. In addition, among these SNP loci, five were identified as having an association with type 2 diabetes risk.

This study demonstrates that genetic studies of glycemic traits can identify type 2 diabetes risk loci. It is essential that there is a continued identification of these loci, which would allow for individuals to undergo more effective genetic predisposition tests for the condition, so that measured steps may be taken to minimalize chances of contracting type 2 diabetes for those individuals.

Link to Article: http://www.nature.com/ng/journal/v42/n2/abs/ng.520.html

Dupris, Josée et al. “New Genetic Loci Implicated in Fasting Glucose Homeostasis and Their Impact on Type 2 Diabetes Risk”. Nature Genetics 42.2 (2010): 105-116.

Genetics of the Pleb Plebis

“Our biggest fear is a power-failure” Dr. Pui-Yan Kwok of the University of California at San Francisco notes, a fear shared by tropical aquarium enthusiasts everywhere. However, unlike amateur aquarists, Dr. Kwok is working on human genetic research on a massive scale. Using recent advances in genetic technology that allows for rapid analysis of a human genome, researchers at Kaiser Permanente in Oakland and at UCSF are working to analyze over 130,000 samples of DNA in order to uncover the roots of genetic disorders and to work out just how it is that some people live longer than others.

This project dwarfs others of its kind. Most genome wide studies work with samples of under 10,000, and possibly by using some previously published data from smaller studies. Access to over 130,000 samples, simply put, will provide an enormous statistical pool from which to draw information. Several advances in technology and shifts in the political winds have allowed this to be possible. Although the Human Genome project, started in the early nineties, took over a decade to sequence a group of under a dozen genomes, this project is working on analyzing 2,500 samples… in one week. Politics have also come in to play, as advances in technology have aligned with the Obama Administration’s resolve to keep science and research well funded. The team received the $25 million grant that made this large scale operation possible from Obama’s Federal Stimulus package, passed last year.

There are three prongs to this endeavor. The first is the collection of samples. For this, Kaiser’s large pool of patients is being tapped. Almost two million patients were asked about participation in 2007, and a large group assented. This large pool was winnowed down to the 130,000 participants, who received little plastic cups in which to spit by mail. The saliva of the participants contained enough genetic material for a full analysis. Dr Kwok’s lab at UCSF will analyze the genomes in order to compare genomes of people with diseases such as cancer and multiple sclerosis to healthy genomes, hopefully to pinpoint the genetic causes. Another UCSF researcher, Nobel laureate Dr. Elizabeth Blackburn, will analyze the genomes with a different aim. Her lab will be measuring the length of the chromosome’s telomeres. Telomeres are bits of DNA on the tops and bottoms of chromosomes that seem to regulate lifespan.

The DNA samples are stored in specialized cardboard boxes at room temperature while they await analysis. Special robots costing a quarter of a million dollars each take the saliva samples and processes them, storing the data. This is where Dr. Kwok’s fear of a power failure comes from, as each array filled with 96 analyzed DNA samples costs $10,000. Although some scientists, such as Dr. David B. Goldstein of Duke University, think the money would be better spent on more specialized research focusing on total sequencing of a smaller number of genomes rather than a large number being scanned for variations, it is hard to argue that the scale of this operation will not produce useful data. Even if the UCSF researchers are unable to glean anything useful from the research, this large amount of data will be available for future studies. This study is a landmark, as genome analysis has typically relied on smaller numbers of genomes self selected by paying for a service, or by researchers just taking small samples of people. The technology has moved to the point where truly large numbers of people’s information can be processed, and this study of 130,000 is just the beginning. Kaiser is currently planning to sample 400,000 more patients over the coming years. This huge pool of genetic material will hopefully provide science and medicine with powerful insights into the way our bodies are built, and more importantly, ways to fix ailing ones.

Article by Sabin Russel of the new york times.Original article can be viewed at:www.nytimes.com/2010/05/30/science/30sfgenome.html

Hutchison-Gilford Progeria Syndrome: Insight Into Normal Human Aging

Hutchison-Gilford Progeria Syndrome is a disease in which children experience very rapid aging. In all cases these children will experience rapid decay in their vascular, muscular, and skeletal systems until they die at about 15 years old usually from cardiovascular problems (stroke or heart attack). The Massachusetts Medical Society enrolled 15 children into this study ranging from ages 1 to 17 years of age, nearly half of the worlds known patients with this syndrome. The stereotypic phenotype we see from these individuals include sclerosis of the skin, joint contractures, bone abnormalities, alopecia (hair loss), and stunted growth. When studying the cardiovascular system they saw weakening heart function, high blood pressure, and hardening/thickening of the arterial walls. All of these problems are seen in normal human aging and if we can better understand the phenotypic malfunctions in Hutchinson-Gilford Progeria Syndrome then we may gain insight into normal human aging and bring us closer to finding ways to slow normal human aging.

The Medical Society also looked at this disease from a genetic standpoint. If you look at the LMNA gene's 12 exons you get two main splice products. Lamin C is encoded by exons 1 to 9 and a portion of exon 10. Lamin A results from alternative splicing which adds exons 11 & 12 and removes the Lamin C-specific portion of exon 10. It is during this splicing which the disease occurs. If LMNA gene is working properly the nuclear structure is maintained, transcription is regulated, there is proper differentiation of mesenchymal cells types (adipose and skeletal muscle tissues), and correct chromatin organization within the nucleus. In Hutchison-Gilford Progeria Syndrome there is a mutation in the LMNA gene where it encodes for Lamin A. At this particular location we see a change from glycine (GGC) to glycine (GGT). This causes an activation of cryptic splice site which leads to truncated proteins. This does not allow for proper nuclear structure (causes nuclear blebbing), disorganizes chromatin placement, and interrupts transcription. The next step in studying this disease is to see if this same malfunction in the LMNA gene occurs over a longer period of time in unaffected humans and if so, we can take steps to delay the onset of normal human aging.

New England Journal of Medicine, 2008, pgs. 592-604. www.nejm.org

With so much variation, how can we make sense of it all?

The field of Evolutionary Genetics focuses on the interplay between genetic events, speciation, and phenotypic diversity. A noticeable part of genetics that has been seen to vary between species is gene expression. Despite this common trend, little research has been performed to assess the extent to which transcription factor (TF) binding differs among individuals of the same species and closely related species, as well as the overarching connection between TF binding and genetic variability. In order to figure out some of the mystery, Maya Kasowski et al. decided to look at the variation in TF binding among humans.

The researchers decided to use 10 individuals (5 of European ancestry, 2 of eastern Asian ancestry, and 3 of Nigerian ancestry) with extensive genetic data already existing for them, as well as one chimpanzee as a point of comparison because of how closely related they are to humans. Once they picked their people, they used chromatin immunoprecipitation plus sequencing (ChIP-seq: For a quick reminder check this out! http://en.wikipedia.org/wiki/Chromatin_immunoprecipitation ) to figure out the binding sites of two TF, RNA polymerase II (Pol II) and nuclear factor kB (NFkB). This two transcription factors were not picked randomly of course! Pol II catalyzes reactions that make the precursors of mRNA, snRNA, and microRNA while NFkB is a key regulator of immune responses as it acts as the last component that actually binds to the DNA to start transcription. As you can see, these factors are very important, and what’s more is that their different binding regions have links to many high interest diseases. For instance, type I diabetes, chronic lymphatic leukemia, and schizophrenia relate to Pol II genes while asthma, Crohn’s disease, and rheumatoid arthritis relate to NFkB.

Overall, the results they found were that differences of 7.5% and 25% exist in TF binding for NfkB and PolII respectively between the individuals they studied, but the estimated value for sequence variation in coding sequences is only 0.025% between humans. Basically, what they found was that there was a very strong role in binding variation in human diversity. When I first read the article, 7.5% and 25% did not seem like large enough numbers, but compared to 0.025% this is a very significant difference that deserves further research. An interesting finding of theirs is that these differences were more likely to be found in variable regions of the genome, such as those involved in immune response. This makes sense because the individuals that had more variability in their immune responses would survive preferentially due to their increased ability to adapt to novel diseases or viruses. Further research after this study could expand upon their studies. How can they apply their findings to human medicine once they recognized the disease loci? Will they now be able to even more accurately explain speciation events and phenotypic diversity? I don’t know what will come of the further research, but the endless possibilities are sure to be central to evolutionary genetic research for years.

Kasowski, M. et al., 2001, Variation in Transcription Factor Binding Among Humans, Science, v. 328, p. 232.

Reconstructing a Mammoth Hemoglobin

The reconstruction of a Mammoth just might be possible! Well not quite yet, but researchers are getting closer and closer. A team led by Kevin L. Campbell of the University of Manitoba in Canada, has reconstructed the Mammoth’s hemoglobin. People usually associate these furry creatures with the frozen arctic; however, they actually originated in the tropics about seven million years ago. Their split from the elephants is what led them to adaptations in the cold northern latitudes. The split occurred in physical appearance such as smaller ears, a thick furry coat, and in protein structure such as hemoglobin.

Hemoglobin is the protein that is responsible for the transport of oxygen from the lungs to the rest of the body. It is an assembly of four globular protein subunits which are made of globin chains and these are tightly associated with a heme (iron) group. In humans, most of our blood contains two alpha chains and two beta chains; however, elephant hemoglobin is slightly different. It is composed of 2 alpha globins chains and 2 fused delta-beta chains. It was assumed that Mammoths also had the same structure of hemoglobin; therefore, with that knowledge Dr. Campbell was able to construct tools necessary to fish out these chains from a 43,000 year old, well preserved mammoth. They discovered that the alpha chains differed from elephants in one of its amino acid units and the beta-delta chain differed in three units. This was all reported to Nature Genetics, because with this type of information, they could potentially reconstruct a mammoth hemoglobin.

The next step for Dr. Campbell and his team was to figure out a way to synthesize copies of the mammoth’s two globin genes. Dr. Campbell came up with a technique to just alter the DNA units of an elephant’s globin genes one by one at the four different sites until it matched that of the mammoth’s. This globin gene was then inserted into bacteria which was then synthesized into the mammoth globin chains. After inserting the required iron atoms, the globin chains were assembled into working hemoglobin molecules. This new development led Dr. Campbell to state, “It’s the same as if I went back 43,000 years in a time machine and took blood from a mammoth!”

This was a significant discovery in proving adaptive mutations for survival. As arteries carry blood down to the feet, they warm up the blood traveling up through the veins. Therefore, with this heat transfer, the blood at the toes are cold which prevents much heat loss. However, oxygen release from the hemoglobin becomes much less efficient at lower temperatures. With the construction discovery of the mammoth’s hemoglobin, scientists were able to determine how such an arctic mammal was capable of survival. The way the mammoth’s hemoglobin had evolved, it allowed for oxygen to be released from hemoglobin much more readily at lower temperatures.

Two years ago, scientists at Penn State University sequenced a large portion of the mammoth genome from a clump of well preserved hair. Now, with this completed reconstruction of their hemoglobin, scientists are getting closer to reconstructing the whole animal. Dr. Campbell states his optimism on the possibility; however, he also says “I’m 42 years old, but I doubt I’ll ever see a living mammoth.” We still have years of research left, but every step is one step closer!

Kevin L Campbell et. Al
Nature Genetics Volume: 42, Pages: 536–540 Year published: (2010)
DOI: doi:10.1038/ng.574 Received 18 December 2009 Accepted 31 March 2010
Published online 02 May 201

Link to article: http://www.nature.com/ng/journal/v42/n6/abs/ng.574.html#/

The Search for the Origin of Our Favorite Canine Companion

The search for the origin of the domesticated dog has been a long process and full of controversy. We all have heard how dogs were domesticated from wolves, but knowing when and where is a bit of a mystery. “New Finding Puts Origins of Dogs in Middle East” by Nicholas Wade reports on a new study that has yet another theory on the origin of dog domestication- the Middle East.
Bridgett M. vonHoldt and Robert K. Wayne of UCLA led a team that analyzed a large collection of wolf and dog DNA from around the world. Using two dog genomes previously sequenced (a poodle and a boxer) they developed a dog SNP chip that was used to scan for variable sites in the DNA of a variety of dogs and wolves and cluster them into groups of who is most related to who. Not only did this allow them to place the origin of the domesticated dog in the Middle East, but also showed that dogs with common functions (such as herding dogs and scent hounds) are closely related- showing that these functions are not an example of convergent evolution but that breeds with a common function are closely related.
This team concluded that dogs were domesticated in the Middle East, and later spread to East Asia (where previous studies have put the origin of domesticated dogs). In Asia, some of the dogs bred with local wolves, part of the reason the genetic evidence is so convoluted. The team also used their SNP chips to scan for areas that showed signatures of selection. There is evidence supporting that the dogs lovable personality and their unique ability to “read” human expression were both selected (whether naturally or artificially) in the dog domestication process.
All theories on the origin of a species must be checked with archeological evidence, especially since most DNA samples taken are from modern dogs and wolves and is only a reflection of what was. A Middle Eastern origin fits the archeological evidence better than the other theories presented. This study puts the origin of a domesticated species, dogs, at the same place of domestication of many other plants and animals. According to this study, dogs were domesticated 15,000 years ago- a time when hunter gathers were converting to more stationary societies. Dogs may not only be our best friends, but what allowed us to settle and grow into what we are today.

P.S: Check out the family tree from this article: http://www.nytimes.com/2010/03/18/science/18dogs.html?scp=6&sq=Dog+DNA&st=nyt

P.S.S. If you search for the study this paper was based on, you can get an even better tree!

Reference:
Wade, Nicholas. "New Finding Puts Origins of Dogs in Middle East." New York Times 17 March 2010: Web. 16 May 2010.

Original Article:
vonHoldt, Bridgett M., John P. Pollinger, Kirk E. Lohmueller, Eunjung Han , and others. "Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication." NATURE 464.8 April 2010: 898-903. Web. 28 April 2010.

CpG methylation influences mutation rates

DNA Sequence Itself Influences Mutation Rate, New Research Indicates

Natural selection, accomplished by mutations and heritability, is the driving force of evolution. Neutral selection defines any region of DNA which is changing at a random rate, and not under any selection preferences. Thus, scientists are usually more interested in those regions which do experience selection, and often overlook the neutral sequences. But what makes these regions neutral? Not all regions under selection are in genes, or affect phenotypic expression; thus why is there neutrality or selection at all?

This paper recognizes that there is a need to look at the neutral mutation rate, since this rate is important in keeping genomic stability. A lot of errors/mutations are caught in the proofreading processes of transcription and replication. Seemingly random, they seem inconsequential. But according to Walser and Furano, mutation rates in mammals differ at methylated cytosines, with 10-50 times more mutations at these sites.

Methylation of cytosine (CpG) in endogenous DNA sequences is critical for many organisms. Euchromatin activation is driven by methylation, and in plants, methylation is indicative of host genome recognition against foreign pathogen DNA. The high CpG rate results from the spontaneous deamination of methyl-C to T and incomplete restoration of the ensuing T:G mismatches to C:Gs (Walser et al. 2010). The concentration and ratio of CpG seems to positively correlate with the rate of mutation. However chemically modified CpG are prone to mutation as well, and the age of the mutation can be assessed.

Interestingly enough, in older inactive retrotransposons latent within the primate genome, the overall mutation rates have dropped and are now neutrally evolving. However this is not due to chromosomal location (by the centromere, etc.), but due to the inherent DNA sequence itself. The article concludes that these methylated areas promote mutations at the methylated sites, as well as the surrounding DNA. Future studies of methylated mutation rates will probably still continue to focus on genomic stability and repair.

Science Daily article: http://www.sciencedaily.com/releases/2010/05/100524092348.htm

Walser J, Furano A. The mutational spectrum of non-CpG DNA varies with CpG content. Genome Research, 2010; DOI: 10.1101/gr.103283.109